An Exact Algorithm to Compute the DCJ Distance for Genomes with Duplicate Genes

  • Mingfu Shao
  • Yu Lin
  • Bernard Moret
Part of the Lecture Notes in Computer Science book series (LNCS, volume 8394)


Computing the edit distance between two genomes is a basic problem in the study of genome evolution. The double-cut-and-join (DCJ) model has formed the basis for most algorithmic research on rearrangements over the last few years. The edit distance under the DCJ model can be computed in linear time for genomes without duplicate genes, while the problem becomes NP-hard in the presence of duplicate genes. In this paper, we propose an ILP (integer linear programming) formulation to compute the DCJ distance between two genomes with duplicate genes. We also provide an efficient preprocessing approach to simplify the ILP formulation while preserving optimality. Comparison on simulated genomes demonstrates that our method outperforms MSOAR in computing the edit distance, especially when the genomes contain long duplicated segments. We also apply our method to assign orthologous gene pairs among human, mouse and rat genomes, where once again our method outperforms MSOAR.


DCJ distance adjacency graph maximum cycle decomposition orthology assignment 


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Copyright information

© Springer International Publishing Switzerland 2014

Authors and Affiliations

  • Mingfu Shao
    • 1
  • Yu Lin
    • 1
    • 2
  • Bernard Moret
    • 1
  1. 1.Laboratory for Computational Biology and BioinformaticsEPFLLausanneSwitzerland
  2. 2.Department of Computer Science and EngineeringUniversity of CaliforniaSan DiegoUSA

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